Tony doesn't use nanotechnology (defined as semi-autonomous machines on a microscopisic scale) in his suit. The smallest independent parts we know the typical suit contained are the tiles described in the 'Iron Manual', and they're about a millimeter or so from edge to edge.

That was true prior to the SKIN armor. The armor Tony designed before Riri took over is nano tech. This is how he could formulate complete new structures out of his armor.